Starting phenix.real_space_refine on Tue Aug 4 12:20:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w07_65495/08_2026/9w07_65495.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1548 2.51 5 N 435 2.21 5 O 525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2508 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 420 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 416 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: D, E, G, H Time building chain proxies: 0.47, per 1000 atoms: 0.19 Number of scatterers: 2508 At special positions: 0 Unit cell: (66.4, 102.09, 33.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 525 8.00 N 435 7.00 C 1548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.12 Conformation dependent library (CDL) restraints added in 64.2 milliseconds 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 44.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 43 removed outlier: 6.569A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER E 42 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.926A pdb=" N GLY E 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.539A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 66 removed outlier: 6.730A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 69 through 70 removed outlier: 6.470A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 82 removed outlier: 6.339A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN E 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR E 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 95 removed outlier: 6.284A pdb=" N SER C 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ALA E 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ALA C 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N THR E 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ALA C 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N PHE E 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY C 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA D 90 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA E 91 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY E 93 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 44 removed outlier: 6.254A pdb=" N GLU G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER H 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.315A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 55 removed outlier: 6.423A pdb=" N THR G 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.451A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.432A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 78 removed outlier: 6.314A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 88 through 96 removed outlier: 8.716A pdb=" N ALA F 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR H 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ALA F 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE H 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA H 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR G 92 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY H 93 " --> pdb=" O THR G 92 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.20 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 465 1.29 - 1.35: 401 1.35 - 1.42: 64 1.42 - 1.48: 423 1.48 - 1.55: 1161 Bond restraints: 2514 Sorted by residual: bond pdb=" C GLY E 41 " pdb=" O GLY E 41 " ideal model delta sigma weight residual 1.236 1.231 0.005 5.30e-03 3.56e+04 1.03e+00 bond pdb=" C GLY C 41 " pdb=" O GLY C 41 " ideal model delta sigma weight residual 1.236 1.231 0.005 5.30e-03 3.56e+04 7.86e-01 bond pdb=" CA THR C 92 " pdb=" CB THR C 92 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.58e-02 4.01e+03 5.83e-01 bond pdb=" CA GLY C 41 " pdb=" C GLY C 41 " ideal model delta sigma weight residual 1.522 1.512 0.010 1.30e-02 5.92e+03 5.71e-01 bond pdb=" CA GLY D 41 " pdb=" C GLY D 41 " ideal model delta sigma weight residual 1.522 1.513 0.010 1.30e-02 5.92e+03 5.37e-01 ... (remaining 2509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 3196 1.21 - 2.42: 180 2.42 - 3.63: 23 3.63 - 4.84: 0 4.84 - 6.05: 6 Bond angle restraints: 3405 Sorted by residual: angle pdb=" CA GLY D 41 " pdb=" C GLY D 41 " pdb=" N SER D 42 " ideal model delta sigma weight residual 115.64 117.30 -1.66 7.90e-01 1.60e+00 4.41e+00 angle pdb=" CA GLY C 41 " pdb=" C GLY C 41 " pdb=" N SER C 42 " ideal model delta sigma weight residual 115.64 117.20 -1.56 7.90e-01 1.60e+00 3.92e+00 angle pdb=" N GLY D 41 " pdb=" CA GLY D 41 " pdb=" C GLY D 41 " ideal model delta sigma weight residual 111.21 113.26 -2.05 1.04e+00 9.25e-01 3.89e+00 angle pdb=" N GLY C 41 " pdb=" CA GLY C 41 " pdb=" C GLY C 41 " ideal model delta sigma weight residual 111.21 113.24 -2.03 1.04e+00 9.25e-01 3.81e+00 angle pdb=" N GLY E 41 " pdb=" CA GLY E 41 " pdb=" C GLY E 41 " ideal model delta sigma weight residual 111.21 113.22 -2.01 1.04e+00 9.25e-01 3.73e+00 ... (remaining 3400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 1272 13.75 - 27.50: 117 27.50 - 41.25: 33 41.25 - 54.99: 12 54.99 - 68.74: 9 Dihedral angle restraints: 1443 sinusoidal: 462 harmonic: 981 Sorted by residual: dihedral pdb=" CA THR F 44 " pdb=" C THR F 44 " pdb=" N GLY F 45 " pdb=" CA GLY F 45 " ideal model delta harmonic sigma weight residual 180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA THR G 44 " pdb=" C THR G 44 " pdb=" N GLY G 45 " pdb=" CA GLY G 45 " ideal model delta harmonic sigma weight residual -180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA THR H 44 " pdb=" C THR H 44 " pdb=" N GLY H 45 " pdb=" CA GLY H 45 " ideal model delta harmonic sigma weight residual 180.00 -163.37 -16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 225 0.026 - 0.053: 104 0.053 - 0.079: 40 0.079 - 0.106: 39 0.106 - 0.132: 42 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA VAL H 49 " pdb=" N VAL H 49 " pdb=" C VAL H 49 " pdb=" CB VAL H 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL G 49 " pdb=" N VAL G 49 " pdb=" C VAL G 49 " pdb=" CB VAL G 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 447 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 82 " -0.004 2.00e-02 2.50e+03 7.72e-03 5.96e-01 pdb=" C VAL D 82 " 0.013 2.00e-02 2.50e+03 pdb=" O VAL D 82 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU D 83 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 82 " 0.004 2.00e-02 2.50e+03 7.46e-03 5.57e-01 pdb=" C VAL F 82 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL F 82 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU F 83 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 82 " 0.004 2.00e-02 2.50e+03 7.41e-03 5.49e-01 pdb=" C VAL H 82 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL H 82 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU H 83 " 0.004 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 871 2.89 - 3.39: 2062 3.39 - 3.89: 3970 3.89 - 4.40: 4084 4.40 - 4.90: 8454 Nonbonded interactions: 19441 Sorted by model distance: nonbonded pdb=" O THR E 72 " pdb=" OG1 THR E 72 " model vdw 2.384 3.040 nonbonded pdb=" O THR C 72 " pdb=" OG1 THR C 72 " model vdw 2.385 3.040 nonbonded pdb=" O THR D 72 " pdb=" OG1 THR D 72 " model vdw 2.385 3.040 nonbonded pdb=" O GLY H 84 " pdb=" OG SER H 87 " model vdw 2.389 3.040 nonbonded pdb=" O GLY F 84 " pdb=" OG SER F 87 " model vdw 2.390 3.040 ... (remaining 19436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2514 Z= 0.192 Angle : 0.640 6.055 3405 Z= 0.370 Chirality : 0.054 0.132 450 Planarity : 0.002 0.008 435 Dihedral : 14.068 68.743 831 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.37), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE C 94 HIS 0.005 0.002 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 ( 2514) covalent geometry : angle 0.63993 / 0.37 ( 3405) hydrogen bonds : bond 0.19372 / 12.91 ( 47) hydrogen bonds : angle 8.47637 / 5.76 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.107 Fit side-chains REVERT: C 43 LYS cc_start: 0.8384 (mttt) cc_final: 0.8102 (mttp) REVERT: C 61 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 62 GLN cc_start: 0.7893 (tt0) cc_final: 0.7278 (tm-30) REVERT: D 43 LYS cc_start: 0.8287 (mttt) cc_final: 0.7836 (mttp) REVERT: D 61 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7155 (mt-10) REVERT: D 62 GLN cc_start: 0.8094 (tt0) cc_final: 0.7894 (tt0) REVERT: D 83 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6885 (mt-10) REVERT: G 96 LYS cc_start: 0.8545 (tttt) cc_final: 0.8307 (tttm) REVERT: E 39 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7118 (mt-10) REVERT: H 38 LEU cc_start: 0.7715 (pt) cc_final: 0.7512 (pp) REVERT: H 96 LYS cc_start: 0.8461 (tttt) cc_final: 0.8242 (tttm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0866 time to fit residues: 6.4338 Evaluate side-chains 57 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN D 62 GLN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093949 restraints weight = 2791.312| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.13 r_work: 0.3135 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2514 Z= 0.276 Angle : 0.658 7.396 3405 Z= 0.354 Chirality : 0.056 0.127 450 Planarity : 0.003 0.011 435 Dihedral : 5.256 17.822 369 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 5.16 % Allowed : 11.11 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.39), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE E 94 HIS 0.010 0.004 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.28 ( 2514) covalent geometry : angle 0.65828 / 0.35 ( 3405) hydrogen bonds : bond 0.03379 / 2.31 ( 47) hydrogen bonds : angle 6.31249 / 4.25 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.055 Fit side-chains REVERT: C 43 LYS cc_start: 0.8933 (mttt) cc_final: 0.8452 (mttp) REVERT: C 61 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7511 (mp0) REVERT: C 62 GLN cc_start: 0.8222 (tt0) cc_final: 0.7381 (tm-30) REVERT: D 43 LYS cc_start: 0.8850 (mttt) cc_final: 0.8095 (mttp) REVERT: D 61 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 62 GLN cc_start: 0.8579 (tt0) cc_final: 0.8366 (tt0) REVERT: G 96 LYS cc_start: 0.8670 (tttt) cc_final: 0.8327 (tttm) REVERT: E 83 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6886 (tm-30) REVERT: H 96 LYS cc_start: 0.8558 (tttt) cc_final: 0.8144 (tttm) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.0651 time to fit residues: 4.9256 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095714 restraints weight = 2771.095| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.12 r_work: 0.3194 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2514 Z= 0.139 Angle : 0.532 6.871 3405 Z= 0.285 Chirality : 0.053 0.133 450 Planarity : 0.002 0.008 435 Dihedral : 4.858 16.360 369 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.57 % Allowed : 16.27 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.41), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 94 HIS 0.007 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 2514) covalent geometry : angle 0.53216 / 0.29 ( 3405) hydrogen bonds : bond 0.02382 / 1.60 ( 47) hydrogen bonds : angle 5.88874 / 3.99 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.111 Fit side-chains REVERT: C 61 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7441 (mp0) REVERT: C 62 GLN cc_start: 0.8214 (tt0) cc_final: 0.7336 (tm-30) REVERT: D 43 LYS cc_start: 0.8796 (mttt) cc_final: 0.8025 (mttp) REVERT: D 61 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 62 GLN cc_start: 0.8538 (tt0) cc_final: 0.8316 (tt0) REVERT: G 96 LYS cc_start: 0.8549 (tttt) cc_final: 0.8188 (tttm) REVERT: E 83 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6785 (tm-30) REVERT: H 96 LYS cc_start: 0.8490 (tttt) cc_final: 0.8120 (tttm) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.0879 time to fit residues: 6.0334 Evaluate side-chains 63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089582 restraints weight = 2833.596| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.14 r_work: 0.3097 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 2514 Z= 0.360 Angle : 0.733 8.808 3405 Z= 0.393 Chirality : 0.059 0.136 450 Planarity : 0.003 0.012 435 Dihedral : 5.524 18.630 369 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 5.95 % Allowed : 16.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.40), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.004 PHE E 94 HIS 0.012 0.005 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.36 ( 2514) covalent geometry : angle 0.73267 / 0.39 ( 3405) hydrogen bonds : bond 0.02986 / 1.98 ( 47) hydrogen bonds : angle 5.96364 / 4.01 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.086 Fit side-chains REVERT: C 61 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7485 (mp0) REVERT: C 62 GLN cc_start: 0.8230 (tt0) cc_final: 0.7457 (tm-30) REVERT: D 43 LYS cc_start: 0.8930 (mttt) cc_final: 0.8138 (mttp) REVERT: D 61 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7312 (mp0) REVERT: D 62 GLN cc_start: 0.8599 (tt0) cc_final: 0.8372 (tt0) REVERT: G 96 LYS cc_start: 0.8768 (tttt) cc_final: 0.8357 (tttm) REVERT: E 83 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6992 (tm-30) REVERT: H 96 LYS cc_start: 0.8701 (tttt) cc_final: 0.8220 (tttm) outliers start: 15 outliers final: 13 residues processed: 70 average time/residue: 0.0883 time to fit residues: 7.0064 Evaluate side-chains 73 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.095839 restraints weight = 2772.929| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3195 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2514 Z= 0.108 Angle : 0.510 7.329 3405 Z= 0.274 Chirality : 0.053 0.133 450 Planarity : 0.002 0.007 435 Dihedral : 4.815 16.845 369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.57 % Allowed : 19.84 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.43), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE E 94 HIS 0.005 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 2514) covalent geometry : angle 0.50965 / 0.27 ( 3405) hydrogen bonds : bond 0.02012 / 1.34 ( 47) hydrogen bonds : angle 5.52693 / 3.72 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.103 Fit side-chains REVERT: C 43 LYS cc_start: 0.8914 (mttt) cc_final: 0.8292 (mttp) REVERT: C 61 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7439 (mp0) REVERT: C 62 GLN cc_start: 0.8239 (tt0) cc_final: 0.7422 (tm-30) REVERT: D 43 LYS cc_start: 0.8919 (mttt) cc_final: 0.8153 (mttp) REVERT: D 61 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7307 (mp0) REVERT: D 62 GLN cc_start: 0.8550 (tt0) cc_final: 0.8341 (tt0) REVERT: G 96 LYS cc_start: 0.8595 (tttt) cc_final: 0.8212 (tttm) REVERT: H 96 LYS cc_start: 0.8563 (tttt) cc_final: 0.8244 (tttm) outliers start: 9 outliers final: 8 residues processed: 61 average time/residue: 0.0962 time to fit residues: 6.6019 Evaluate side-chains 62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.120275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097826 restraints weight = 2761.389| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.18 r_work: 0.3232 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2514 Z= 0.088 Angle : 0.475 7.314 3405 Z= 0.254 Chirality : 0.053 0.133 450 Planarity : 0.001 0.007 435 Dihedral : 4.456 16.344 369 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.37 % Allowed : 17.86 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.44), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE E 94 HIS 0.005 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 2514) covalent geometry : angle 0.47486 / 0.25 ( 3405) hydrogen bonds : bond 0.01882 / 1.22 ( 47) hydrogen bonds : angle 5.21114 / 3.50 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.057 Fit side-chains REVERT: C 61 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7431 (mp0) REVERT: C 62 GLN cc_start: 0.8183 (tt0) cc_final: 0.7355 (tm-30) REVERT: D 43 LYS cc_start: 0.8893 (mttt) cc_final: 0.8115 (mttp) REVERT: D 61 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7227 (mp0) REVERT: D 62 GLN cc_start: 0.8506 (tt0) cc_final: 0.8291 (tt0) REVERT: G 96 LYS cc_start: 0.8544 (tttt) cc_final: 0.8135 (tttm) REVERT: E 83 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6849 (tm-30) REVERT: H 96 LYS cc_start: 0.8476 (tttt) cc_final: 0.8106 (tttm) outliers start: 11 outliers final: 11 residues processed: 65 average time/residue: 0.0820 time to fit residues: 5.9888 Evaluate side-chains 68 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 9.9990 chunk 15 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098030 restraints weight = 2752.562| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.18 r_work: 0.3201 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2514 Z= 0.126 Angle : 0.505 7.311 3405 Z= 0.270 Chirality : 0.053 0.134 450 Planarity : 0.002 0.007 435 Dihedral : 4.559 16.709 369 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.16 % Allowed : 17.06 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.45), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE E 94 HIS 0.006 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 2514) covalent geometry : angle 0.50492 / 0.27 ( 3405) hydrogen bonds : bond 0.01936 / 1.24 ( 47) hydrogen bonds : angle 5.21641 / 3.51 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.096 Fit side-chains REVERT: C 61 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7486 (mp0) REVERT: C 62 GLN cc_start: 0.8233 (tt0) cc_final: 0.7466 (tm-30) REVERT: D 43 LYS cc_start: 0.8988 (mttt) cc_final: 0.8251 (mttp) REVERT: D 61 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7309 (mp0) REVERT: D 62 GLN cc_start: 0.8513 (tt0) cc_final: 0.8303 (tt0) REVERT: G 96 LYS cc_start: 0.8652 (tttt) cc_final: 0.8246 (tttm) REVERT: E 83 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6954 (tm-30) REVERT: H 96 LYS cc_start: 0.8581 (tttt) cc_final: 0.8259 (tttm) outliers start: 13 outliers final: 13 residues processed: 64 average time/residue: 0.0967 time to fit residues: 6.9603 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096473 restraints weight = 2784.536| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.20 r_work: 0.3206 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2514 Z= 0.113 Angle : 0.491 7.129 3405 Z= 0.264 Chirality : 0.053 0.134 450 Planarity : 0.002 0.008 435 Dihedral : 4.513 16.724 369 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.16 % Allowed : 17.86 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.46), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 94 HIS 0.006 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 2514) covalent geometry : angle 0.49134 / 0.26 ( 3405) hydrogen bonds : bond 0.01878 / 1.20 ( 47) hydrogen bonds : angle 5.18769 / 3.49 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.094 Fit side-chains REVERT: C 61 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7445 (mp0) REVERT: C 62 GLN cc_start: 0.8235 (tt0) cc_final: 0.7392 (tm-30) REVERT: D 43 LYS cc_start: 0.8918 (mttt) cc_final: 0.8131 (mttp) REVERT: D 61 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7247 (mp0) REVERT: D 62 GLN cc_start: 0.8516 (tt0) cc_final: 0.8299 (tt0) REVERT: G 96 LYS cc_start: 0.8575 (tttt) cc_final: 0.8136 (tttm) REVERT: E 83 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6879 (tm-30) REVERT: H 96 LYS cc_start: 0.8515 (tttt) cc_final: 0.8171 (tttm) outliers start: 13 outliers final: 12 residues processed: 65 average time/residue: 0.0941 time to fit residues: 6.8973 Evaluate side-chains 69 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094632 restraints weight = 2852.419| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.23 r_work: 0.3177 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2514 Z= 0.154 Angle : 0.529 7.311 3405 Z= 0.283 Chirality : 0.053 0.135 450 Planarity : 0.002 0.009 435 Dihedral : 4.676 17.117 369 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.76 % Allowed : 18.25 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.46), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE E 94 HIS 0.007 0.003 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 2514) covalent geometry : angle 0.52859 / 0.28 ( 3405) hydrogen bonds : bond 0.02014 / 1.29 ( 47) hydrogen bonds : angle 5.27864 / 3.55 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.099 Fit side-chains REVERT: C 61 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7443 (mp0) REVERT: C 62 GLN cc_start: 0.8236 (tt0) cc_final: 0.7394 (tm-30) REVERT: D 43 LYS cc_start: 0.8954 (mttt) cc_final: 0.8163 (mttp) REVERT: D 61 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7261 (mp0) REVERT: D 62 GLN cc_start: 0.8539 (tt0) cc_final: 0.8324 (tt0) REVERT: G 96 LYS cc_start: 0.8614 (tttt) cc_final: 0.8181 (tttm) REVERT: E 83 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6855 (tm-30) REVERT: H 96 LYS cc_start: 0.8540 (tttt) cc_final: 0.8209 (tttm) outliers start: 12 outliers final: 12 residues processed: 62 average time/residue: 0.0940 time to fit residues: 6.5267 Evaluate side-chains 67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 25 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099185 restraints weight = 2814.895| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.22 r_work: 0.3259 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 2514 Z= 0.072 Angle : 0.448 6.921 3405 Z= 0.242 Chirality : 0.052 0.131 450 Planarity : 0.001 0.007 435 Dihedral : 4.338 15.899 369 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.57 % Allowed : 19.84 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.47), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE D 94 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00146 / 0.07 ( 2514) covalent geometry : angle 0.44796 / 0.24 ( 3405) hydrogen bonds : bond 0.01727 / 1.11 ( 47) hydrogen bonds : angle 5.06314 / 3.41 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 726 Ramachandran restraints generated. 363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.092 Fit side-chains REVERT: C 61 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7420 (mp0) REVERT: C 62 GLN cc_start: 0.8223 (tt0) cc_final: 0.7384 (tm-30) REVERT: C 83 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7015 (tp30) REVERT: D 43 LYS cc_start: 0.8898 (mttt) cc_final: 0.8131 (mttp) REVERT: D 61 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7201 (mp0) REVERT: D 62 GLN cc_start: 0.8499 (tt0) cc_final: 0.8290 (tt0) REVERT: G 66 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8233 (t) REVERT: G 96 LYS cc_start: 0.8558 (tttt) cc_final: 0.8109 (tttm) REVERT: H 96 LYS cc_start: 0.8440 (tttt) cc_final: 0.8082 (tttm) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.0931 time to fit residues: 6.6338 Evaluate side-chains 63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.091888 restraints weight = 2857.992| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.20 r_work: 0.3132 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2514 Z= 0.267 Angle : 0.629 8.022 3405 Z= 0.336 Chirality : 0.056 0.133 450 Planarity : 0.003 0.011 435 Dihedral : 4.976 18.504 369 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.37 % Allowed : 19.44 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.46), residues: 363 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHE E 94 HIS 0.009 0.004 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 ( 2514) covalent geometry : angle 0.62902 / 0.34 ( 3405) hydrogen bonds : bond 0.02354 / 1.51 ( 47) hydrogen bonds : angle 5.45209 / 3.68 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 858.54 seconds wall clock time: 15 minutes 23.54 seconds (923.54 seconds total)